mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 526,792 | A→C | 17.3% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 15.3% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| JC | 712,530 | Δ3 bp | 1.8% | coding (271‑273/765 nt) | ybfF ← | acyl‑CoA esterase |
| RA | 723,130 | C→A | 11.8% | V429L (GTG→TTG) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| JC | 1,013,886 | Δ4 bp | 1.8% | coding (628‑631/1641 nt) | pqiB → | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| RA | 1,097,158 | C→T | 13.9% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,196,220 | C→T | 6.8% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 7.2% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 7.2% | L375L (TTA→CTA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 6.7% | L375L (TTA→TTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | 5.7% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | 6.6% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | 5.7% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,292 | C→T | 5.7% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,304 | G→A | 6.3% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,287,037 | C→T | 8.0% | intergenic (+511/+50) | narI → / ← tpr | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein |
| RA | 1,311,197 | G→T | 13.5% | E37* (GAA→TAA) | tonB → | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| RA | 1,466,210 | G→A | 6.5% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,276 | T→C | 6.9% | pseudogene (885/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 7.1% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 9.3% | pseudogene (1194/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,711 | T→C | 5.2% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 100% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,753,712 | A→T | 7.2% | I40N (ATT→AAT) | ydhV ← | putative oxidoreductase subunit |
| JC JC | 1,907,448 | IS5 (+) +4 bp | 100% | coding (141‑144/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,523 | G→C | 8.2% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,798 | T→C | 6.8% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC | 2,347,240 | Δ88 bp | 67.7% | intergenic (+90/‑57) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| RA | 2,967,727 | Δ1 bp | 100% | coding (708/2247 nt) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,270,143 | C→T | 9.7% | intergenic (+541/+482) | yhaC → / ← garK | pentapetide repeats‑related protein/glycerate kinase I |
| RA | 3,560,455 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,815,801 | Δ1 bp | 100% | intergenic (‑33/+33) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,183,621 | G→C | 8.5% | E793Q (GAA→CAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,185,642 | G→A | 11.0% | R98H (CGC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,186,542 | A→T | 78.6% | K398M (AAG→ATG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,155 | T→C | 8.6% | intergenic (+361/+281) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 29.1% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 30.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 31.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 16.0% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 7.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 9.6% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,088 | T→G | 6.5% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,141 | T→C | 5.8% | intergenic (‑400/+258) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 526980 | 529404 | 2425 | 62 [61] | [61] 62 | [rhsD]–ybbD | [rhsD], ybbC, rhsH, ybbD |
| * | * | ÷ | NC_000913 | 582627 | 584802 | 2176 | 63 [61] | [60] 62 | [ybcY]–[ompT] | [ybcY], ybcY, tfaX, appY, [ompT] |
| * | * | ÷ | NC_000913 | 735880 | 736890 | 1011 | 62 [61] | [58] 62 | [ybfC]–[ybfL] | [ybfC], ybfQ, [ybfL] |
| * | * | ÷ | NC_000913 | 1196551 | 1198770 | 2220 | 63 [60] | [59] 62 | ymfD–[lit] | ymfD, ymfE, [lit] |
| * | * | ÷ | NC_000913 | 1210961 | 1212897 | 1937 | 62 [60] | [59] 62 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1215354 | 1216829 | 1476 | 64 [59] | [59] 63 | [bluF]–[ymgC] | [bluF], ycgZ, ymgA, ariR, [ymgC] |
| * | * | ÷ | NC_000913 | 1230133 | 1230759 | 627 | 63 [61] | [61] 62 | [hlyE] | [hlyE] |
| * | * | ÷ | NC_000913 | 1299192 | 1301117 | 1926 | 62 [61] | [61] 62 | [ychE] | [ychE] |
| * | * | ÷ | NC_000913 | 1526695 | 1527796 | 1102 | 62 [61] | [59] 62 | [yncG]–yncH | [yncG], yncH |
| * | * | ÷ | NC_000913 | 1529886 | 1530610 | 725 | 62 [59] | [61] 65 | [rhsE]–[yncI] | [rhsE], ydcD, [yncI] |
| * | * | ÷ | NC_000913 | 1544188 | 1545438 | 1251 | 64 [61] | [61] 63 | yddK–[yddK] | yddK, [yddK] |
| * | * | ÷ | NC_000913 | 1583440 | 1584232 | 793 | 62 [60] | [61] 65 | [ydeO]–[ydeP] | [ydeO], safA, [ydeP] |
| * | * | ÷ | NC_000913 | 1598061 | 1598579 | 519 | 66 [61] | [61] 62 | yneO/lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
| * | * | ÷ | NC_000913 | 1754548 | 1755526 | 979 | 62 [59] | [61] 62 | ydhZ | ydhZ |
| * | * | ÷ | NC_000913 | 1978219 | 1979738 | 1520 | 63 [61] | [59] 63 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2033349 | 2034183 | 835 | 64 [58] | [61] 63 | [yedR]–[yedS] | [yedR], [yedS] |
| * | * | ÷ | NC_000913 | 2103125 | 2104289 | 1165 | 63 [61] | [61] 62 | [wbbL]–[wbbK] | [wbbL], [wbbK] |
| * | * | ÷ | NC_000913 | 2105025 | 2107498 | 2474 | 63 [58] | [55] 62 | [wbbJ]–[glf] | [wbbJ], wbbI, wbbH, [glf] |
| * | * | ÷ | NC_000913 | 2455517 | 2456249 | 733 | 65 [61] | [60] 62 | [yfcV] | [yfcV] |
| * | * | ÷ | NC_000913 | 2462829 | 2464424 | 1596 | 63 [59] | [61] 62 | yfdF–[mlaA] | yfdF, [mlaA] |
| * | * | ÷ | NC_000913 | 2469019 | 2470824 | 1806 | 62 [57] | [60] 63 | [gtrB]–[tfaS] | [gtrB], gtrS, [tfaS] |
| * | * | ÷ | NC_000913 | 2773217 | 2775499 | 2283 | 65 [60] | [61] 63 | yfjW | yfjW |
| * | * | ÷ | NC_000913 | 2884078 | 2884593 | 516 | 62 [61] | [61] 64 | [casA]–[ygcB] | [casA], [ygcB] |
| * | * | ÷ | NC_000913 | 3267772 | 3269821 | 2050 | 62 [60] | [57] 63 | yhaB–yhaC | yhaB, yhaC |
| * | * | ÷ | NC_000913 | 3581611 | 3584941 | 3331 | 66 [60] | [55] 63 | [yhhY]–[yrhB] | [yhhY], yhhZ, yrhA, insA, insB1, yrhA, [yrhB] |
| * | * | ÷ | NC_000913 | 3766227 | 3767155 | 929 | 62 [58] | [61] 62 | [rhsA]–[yibA] | [rhsA], [yibA] |
| * | * | ÷ | NC_000913 | 3768916 | 3770273 | 1358 | 62 [57] | [61] 62 | [yibW]–[yibH] | [yibW], yibW, yibV, yibV, yibU, yibU, [yibH] |
| * | * | ÷ | NC_000913 | 3796846 | 3800614 | 3769 | 62 [61] | [59] 65 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3800617 | 3803420 | 2804 | 65 [59] | [61] 64 | [waaY]–[waaB] | [waaY], waaR, waaO, [waaB] |
| * | * | ÷ | NC_000913 | 3803984 | 3805358 | 1375 | 65 [61] | [61] 62 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4043841 | 4044389 | 549 | 62 [60] | [61] 62 | [dsbA]–[yihF] | [dsbA], [yihF] |
| * | * | ÷ | NC_000913 | 4078426 | 4079693 | 1268 | 63 [61] | [61] 62 | [yiiD]–yiiE | [yiiD], yiiE |
| * | * | ÷ | NC_000913 | 4221572 | 4222741 | 1170 | 64 [61] | [44] 64 | [arpA] | [arpA] |
| * | * | ÷ | NC_000913 | 4475300 | 4477250 | 1951 | 62 [57] | [58] 63 | [tabA]–[yjgL] | [tabA], [yjgL] |
| * | * | ÷ | NC_000913 | 4542445 | 4543059 | 615 | 63 [59] | [58] 67 | [fimE] | [fimE] |
| * | * | ÷ | NC_000913 | 4556260 | 4556872 | 613 | 62 [60] | [60] 62 | [yjiC] | [yjiC] |
| * | * | ÷ | NC_000913 | 4571600 | 4572757 | 1158 | 68 [61] | [61] 63 | yjiS–[yjiT] | yjiS, [yjiT] |
| * | * | ÷ | NC_000913 | 4602922 | 4603689 | 768 | 62 [61] | [61] 63 | [yjjQ] | [yjjQ] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 373065 | 136 (1.070) | 3 (0.030) | 3/522 | NT | 2.3% | coding (145/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding |
| ? | NC_000913 | = 373047 | 133 (1.120) | coding (127/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 7 (0.060) | 6/540 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 62 (0.490) | 39 (0.330) | 36/526 | NT | 42.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 48 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 56 (0.440) | 54 (0.450) | 44/526 | NT | 51.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 48 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2705894 | 154 (1.210) | 3 (0.020) | 3/540 | NT | 2.0% | coding (1231/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase |
| ? | NC_000913 | = 2705947 | 139 (1.130) | coding (1178/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase | |||||
| * | ? | NC_000913 | 2777562 = | 118 (0.930) | 3 (0.020) | 3/540 | NT | 2.6% | coding (110/330 nt) | ypjF | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| ? | NC_000913 | 2777586 = | 109 (0.890) | coding (134/330 nt) | ypjF | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system | |||||
| * | ? | NC_000913 | = 2945962 | NA (NA) | 3 (0.020) | 3/544 | NT | NA | noncoding (67/97 nt) | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 2945992 | NA (NA) | noncoding (97/97 nt) | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 3248814 = | 134 (1.050) | 5 (0.040) | 4/538 | NT | 3.8% | coding (376/384 nt) | mzrA | modulator of EnvZ/OmpR regulon |
| ? | NC_000913 | 3248839 = | 124 (1.010) | intergenic (+17/‑130) | mzrA/yqjC | modulator of EnvZ/OmpR regulon/DUF1090 family putative periplasmic protein | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 3 (0.020) | 3/528 | NT | 3.5% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409235 = | 82 (0.680) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||